chrX-71232794-C-A

Variant names:

• chrX-71232794-C-A
• rs17311899

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.48 in 110,134 control chromosomes in the GnomAD database, including 12,255 homozygotes. There are 15,286 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (12255 hom., 15286 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.480 AC: 52824 AN: 110083 Hom.: 12240 Cov.: 22

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.476

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.480 AC: 52899 AN: 110134 Hom.: 12255 Cov.: 22 AF XY: 0.472 AC XY: 15286 AN XY: 32408

African (AFR) AF: 0.885 AC: 26727 AN: 30211

American (AMR) AF: 0.554 AC: 5670 AN: 10242

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 708 AN: 2625

East Asian (EAS) AF: 0.716 AC: 2479 AN: 3461

South Asian (SAS) AF: 0.518 AC: 1346 AN: 2599

European-Finnish (FIN) AF: 0.235 AC: 1363 AN: 5797

Middle Eastern (MID) AF: 0.332 AC: 71 AN: 214

European-Non Finnish (NFE) AF: 0.259 AC: 13665 AN: 52823

Other (OTH) AF: 0.484 AC: 723 AN: 1494

Alfa AF: 0.339 Hom.: 37035

Bravo AF: 0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17311899; hg19: chrX-70452644;